On Tue, 2014-12-09 at 00:47 +0800, Ya Gao wrote:
> Dear all,
>
> I want to perform a simulation with amoebapro13 force field and amoeba
> water model using pmemd.amoeba in amber14.
>
> The system is myoglobin, which is placed in a cubic water box using
> solvatebox with 2 Cl- ions to neutralize the system.
>
> The correct pdb.xyz file can be generated using pdbxyz.x in tinker-6.3.3.
>
> However, when I move to the next step to generate the .analout file, there
> is a error and couldn't generate the correct .analout file.
>
> I checked the input and output files carefully, and found that the error is
> caused due to the Cl- ions.
>
> I tested to remove the ions from the pdb file, and the corresponding
> correct .analout file can be generated.
>
> So can anybody give me some help in dealing with the system with ions using
> tinker ?
Tinker _should_ recognize ions. If you look at amoebapro13.prm, you'll
see the following lines:
atom 255 51 Mg+ "Magnesium Ion Mg+2" 12 24.305 0
atom 256 52 Ca+ "Calcium Ion Ca+2" 20 40.078 0
atom 257 53 Zn+ "Zinc Ion Zn+2" 30 65.390 0
atom 258 54 Cl- "Chloride Ion Cl-" 17 35.453 0
and then again at the bottom:
biotype 2004 K "Potassium Ion" 251
biotype 2005 MG "Magnesium Ion" 255
biotype 2006 CA "Calcium Ion" 256
biotype 2007 CL "Chloride Ion" 258
What I suspect is happening is that the Chloride atom type isn't named
correctly for Tinker to recognize it. Try experimenting with different
names for the chlorine residue and atoms, like Cl- and CL (I'm not quite
sure what tinker uses the "biotype" vs. "atom" records for), and perhaps
with different justifications (e.g., left-justified in the 4-letter
space assigned for atom and residue names).
If you are still having trouble, can you send me your files off-list so
I can take a look? The easier you make it for me to reproduce your
problem, the faster I will be able to help debug.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Dec 08 2014 - 10:30:02 PST
